The potential for preservation of thecosome pteropods is thought to be largely governed by the chemical stability of their delicate aragonitic shells in seawater. However, sediment trap studies have found that significant carbonate dissolution can occur above the carbonate saturation horizon. Here we present the results from experiments conducted on two cruises to the Scotia Sea to directly test whether the breakdown of the organic pteropod body influences shell dissolution. We find that, on the timescales of three to thirteen days, the oxidation of organic matter within the shells of dead pteropods is a stronger driver of shell dissolution than the saturation state of seawater. Three to four days after death, shells became milky white and nano‐SEM images reveal smoothing of internal surface features and increased shell porosity, both indicative of aragonite dissolution. These findings have implications for the interpretation of the condition of pteropod shells from sediment traps and the fossil record, as well as for understanding the processes controlling particulate carbonate export from the surface ocean.